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GotCloud: Binary Releases (view source)

Revision as of 11:21, 10 December 2012

1,014 bytes removed ,  11:21, 10 December 2012
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<code>
 
<code>
−
   biopipe-align_M.m_amd64.deb          aligner
+
   gotcloud-bin_M.m_amd64.deb          aligner and umake
−
  biopipe-umake_M.n_amd64.deb          umake
+
   gotcloud-test_M.n_amd64.deb         test for software
−
   biopipe-testalign_M.n_amd64.deb
  −
  biopipe-testumake_M.n_amd64.deb
   
</code>
 
</code>
   Line 26: Line 24:  
   <b>mkdir debs</b>
 
   <b>mkdir debs</b>
 
   <b>cd debs</b>
 
   <b>cd debs</b>
−
   <b>wget ftp://share.sph.umich.edu/biopipe/\*.deb</b>
+
   <b>wget ftp://share.sph.umich.edu/gotcloud/gotcloud/\*.deb</b>
 
   
 
   
 
   #  Another way:
 
   #  Another way:
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   ftp> <b>prompt</b>
 
   ftp> <b>prompt</b>
 
   Interactive mode off.
 
   Interactive mode off.
−
   ftp> <b>cd biopipe</b>
+
   ftp> <b>cd gotcloud</b>
 
   250 Directory successfully changed.
 
   250 Directory successfully changed.
−
   ftp> <b>mget biopipe*.deb</b>
+
   ftp> <b>mget gotcloud*.deb</b>
 
   ftp> <b>quit</b>
 
   ftp> <b>quit</b>
 
   221 Goodbye.
 
   221 Goodbye.
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<code>
 
<code>
−
   <b>sudo dpkg -i debs/biopipe-align_*_amd64.deb</b>
+
   <b>sudo dpkg -i debs/gotcloud-bin_*_amd64.deb</b>
−
   Selecting previously unselected package biopipe-align.
+
   Selecting previously unselected package gotcloud-bin.
 
   (Reading database ... 25372 files and directories currently installed.)
 
   (Reading database ... 25372 files and directories currently installed.)
−
   Unpacking biopipe-align (from .../biopipe-align_M.n_amd64.deb) ...
+
   Unpacking gotcloud-bin (from .../gotcloud-bin_1.0_amd64.deb) ...
−
   Setting up biopipe-align (M.n) ...
+
   Setting up gotcloud-bin (1.0) ...
−
  Created symlink '/usr/local/bin/gen_biopipeline.pl' to make running the aligner easier.
   
   #============================================================
 
   #============================================================
 
   #  'java' is not installed, do 'sudo apt-get install java-common default-jre'
 
   #  'java' is not installed, do 'sudo apt-get install java-common default-jre'
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   #  'libssl0.9.8' is not installed, do 'sudo apt-get install libssl0.9.8'
 
   #  'libssl0.9.8' is not installed, do 'sudo apt-get install libssl0.9.8'
 
   #============================================================
 
   #============================================================
−
   #============================================================
+
   ...
−
  #  '/usr/local/biopipe/test/align' does not exist so you cannot test this install
  −
  #  Install it by doing 'sudo dpkg -i biopipe-testalign*.deb'
  −
  #============================================================
   
</code>
 
</code>
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<code>
 
<code>
−
   <b>sudo apt-get install make libssl0.9.8 java-common default-jre</b>
+
  <b>sudo apt-get update</b>
 +
   <b>sudo apt-get install java-common default-jre make libssl0.9.8</b>
 
</code>
 
</code>
   −
Finally, install the other packages
  −
  −
<code>
  −
  <b>sudo dpkg -i debs/biopipe-umake_*_amd64.deb</b>
  −
  Selecting previously deselected package biopipe-umake.
  −
  (Reading database ... 98799 files and directories currently installed.)
  −
  Unpacking biopipe-umake (from .../biopipe-umake_M.n_amd64.deb) ...
  −
  Setting up biopipe-umake (M.n) ...
  −
  Created symlink '/usr/local/bin/umake.pl' to make running umake easier.
  −
  Good, you appear to have 'make' installed
  −
  Good, you appear to have 'libssl' installed at the correct level
  −
  #============================================================
  −
  #  '/usr/local/biopipe/test/umake' does not exist so you cannot test this install
  −
  #  Install it by doing 'sudo dpkg -i biopipe-testumake_*.deb'
  −
  #============================================================
  −
</code>
      
'''Testing the Installation'''
 
'''Testing the Installation'''
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The tests run within a few minutes and are self checking, so unless you see obvious errors,
 
The tests run within a few minutes and are self checking, so unless you see obvious errors,
 
you can be reasonably sure everything is set up properly.
 
you can be reasonably sure everything is set up properly.
−
You only need to do this once, unless you have made signifcant changes to your Unix system.
+
You only need to do this once, unless you have made significant changes to your Unix system.
    
<code>   
 
<code>   
−
   <b>sudo dpkg -i debs/biopipe-test*_amd64.deb</b>
+
   <b>sudo dpkg -i debs/gotcloud-test*_amd64.deb</b>
−
   Unpacking biopipe-testalign (from .../biopipe-testalign_M.n_amd64.deb) ...
+
   Selecting previously unselected package gotcloud-test.
−
  Selecting previously deselected package biopipe-testumake.
+
  (Reading database ... 27376 files and directories currently installed.)
−
   Unpacking biopipe-testumake (from .../biopipe-testumake_M.n_amd64.deb) ...
+
   Unpacking gotcloud-test (from .../gotcloud-test_1.0_amd64.deb) ...
−
   Setting up biopipe-testalign (M.n) ...
+
   Setting up gotcloud-test (1.0) ...
−
   To test the pipeline, run:
+
  #======================================================================
 +
  #  GotCloud README
 +
  #======================================================================
 +
   To test the GotCloud aligner, run:
 +
    bin/gen_biopipeline.pl --test ~/testalign
 +
  This will create/clear the output directory ~/testalign.
 +
  Test results and a log file are put in this directory.
 +
  Results are self-checked and if errors should occur, it will be obvious.
 
    
 
    
−
    /usr/local/biopipe/bin/gen_biopipeline.pl --test ~/testalign
+
   To test the GotCloud umake, run:
−
 
+
     bin/umake.pl --test ~/testumake
−
  This will remove the contents of ~/testalign and then run
+
   This will create/clear the output directory ~/testumake.
−
  the aligner test case. The output is verified so you know if
+
   Test results and a log file are put in this directory.
−
  anything failed or not.
+
   Results are self-checked and if errors should occur, it will be obvious.
−
 
+
 
−
  Setting up biopipe-testumake (M.n) ...
  −
   To test umake, run:
  −
 
  −
     /usr/local/biopipe/bin/umake.pl --test ~/testumake
  −
 
  −
   This will remove the contents of ~/testumake and then run
  −
   the umake test case. The output is verified so you know if
  −
   anything failed or not.
   
</code>
 
</code>
   −
Login as a normal user (not as root) and do:
+
Login as a normal user (ubuntu, not as root) and do:
    
<code>
 
<code>
−
   #  Test the aligner (fast, about 3 minutes)
+
   #  Test the aligner (about 2 minutes)
−
   <b>/usr/local/biopipe/bin/gen_biopipeline.pl --test ~/testalign</b>
+
   <b>/usr/local/gotcloud/bin/gen_biopipeline.pl --test ~/testalign</b>
 
   rm -rf ~/testalign              # If no error
 
   rm -rf ~/testalign              # If no error
 
    
 
    
−
   #  Test umake  (longer, about 15 minutes)
+
   #  Test umake  (about 7 minutes)
−
   <b>/usr/local/biopipe/bin/umake.pl --test ~/testumake</b>
+
   <b>/usr/local/gotcloud/bin/umake.pl --test ~/testumake</b>
 
   rm -rf ~/testumake              # If no error
 
   rm -rf ~/testumake              # If no error
 
</code>
 
</code>
Terry Gliedt
283

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Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/6083"

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